Covalent bond fragmentation suitable to describe solids in the fragment molecular orbital method.
To improve the accuracy of the fragment molecular orbital method (FMO), we introduce a new fragmentation scheme based on using frozen orbitals to describe fractioned bonds. By applying this scheme to a set of polyalanine systems of up to 40 residues for the alpha-helix and beta-strand isomers, we established its accuracy, which is considerably improved compared to the original hybrid orbital projection method used for detaching bonds in FMO. For instance, at the two-body FMO expansion with the 6-311G* basis set, the error was typically reduced 2-4 times, and for 6-31G* the accuracy increase was even larger (10 times in terms of the maximum error). For the Trp-cage protein (PDB file 1L2Y) with many charged residues, a fairly large error was observed, which was shown to become small with a larger fragment size or at the three-body level. Consequently, we applied the new scheme to the adsorption of toluene and phenol on a faujasite zeolite, and we demonstrated that good accuracy can be achieved in reproducing ab initio results.
Fedorov
Dmitri G
DG
Research Institute for Computational Sciences, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan. d.g.fedorov@aist.go.jp
Jensen
Jan H
JH
Deka
Ramesh C
RC
Kitaura
Kazuo
K
D000327:Adsorption; D010455:Peptides / Q000737:chemistry; D019800:Phenol / Q000737:chemistry; D011789:Quantum Theory; D013816:Thermodynamics; D014050:Toluene / Q000737:chemistry; D017641:Zeolites / Q000737:chemistry
D010455:Peptides; D017641:Zeolites; D019800:Phenol; D014050:Toluene